A Method for Genome Comparisons and Hybridization Studies Using Known Megabase-Scale DNA Sequences as a Reference

We present a method for genome comparisons and high-resolution hybridization analyses using megabase stretches of known DNA sequences as a reference. The method employs two-dimensional gel electrophoresis, separating genomic segments cut with different restriction endonucleases in the first and seco...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 1997-08, Vol.43 (3), p.307-315
Main Authors: Qiu, Ping, Kupfer, Kenneth C., Garrard, William T.
Format: Article
Language:English
Subjects:
Biological and medical sciences
Chromosome Walking - methods
Chromosomes, Fungal
Computer Graphics
Diverse techniques
DNA - analysis
DNA Restriction Enzymes - metabolism
Electrophoresis, Gel, Two-Dimensional
Filtration - instrumentation
Fundamental and applied biological sciences. Psychology
Genes, Fungal
Image Processing, Computer-Assisted
In Situ Hybridization - methods
Molecular and cellular biology
Nucleic Acid Hybridization - methods
Reference Values
Research Design
Saccharomyces cerevisiae - genetics
Sequence Analysis, DNA - standards
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Summary:We present a method for genome comparisons and high-resolution hybridization analyses using megabase stretches of known DNA sequences as a reference. The method employs two-dimensional gel electrophoresis, separating genomic segments cut with different restriction endonucleases in the first and second dimensions, to generate filters suitable for image analysis and repeated nucleic acid hybridizations. The corresponding two-dimensional pattern is computed from the reference nucleotide sequence and matched to the observed pattern, thereby identifying each fragment on the filter; at the same time the technique uncovers discrepancies from the reference sequence. This permits genome comparisons as well as automated identification and quantification of hybridization patterns with various probes. The technique is illustrated by an analysis ofSaccharomyces cerevisiaechromosome IX.
ISSN:0888-7543
1089-8646
DOI:10.1006/geno.1997.4804